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This is the development version of PhosR; for the stable release version, see PhosR.

A set of methods and tools for comprehensive analysis of phosphoproteomics data

Bioconductor version: Development (3.20)

PhosR is a package for the comprenhensive analysis of phosphoproteomic data. There are two major components to PhosR: processing and downstream analysis. PhosR consists of various processing tools for phosphoproteomics data including filtering, imputation, normalisation, and functional analysis for inferring active kinases and signalling pathways.

Author: Pengyi Yang [aut], Taiyun Kim [aut, cre], Hani Jieun Kim [aut]

Maintainer: Taiyun Kim <taiyun.kim91 at>

Citation (from within R, enter citation("PhosR")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

An introduction to PhosR package HTML R Script
Reference Manual PDF


biocViews Proteomics, ResearchField, Software
Version 1.15.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License GPL-3 + file LICENSE
Depends R (>= 4.2.0)
Imports ruv, e1071, dendextend, limma, pcaMethods, stats, RColorBrewer, circlize, dplyr, igraph, pheatmap, preprocessCore, tidyr, rlang, graphics, grDevices, utils, SummarizedExperiment, methods, S4Vectors, BiocGenerics, ggplot2, GGally, ggdendro, ggpubr, network, reshape2, ggtext, stringi
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Suggests testthat, knitr, rgl, sna, ClueR, directPA, rmarkdown,,, reactome.db, annotate, BiocStyle, stringr, calibrate
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Source Package PhosR_1.15.0.tar.gz
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